Plasmids found in the natural environment have various systems to enable their maintenance in bacteria and propagation between bacteria.
During the process of adapting plasmids for synthetic use various functions were removed such as those responsible for propagation, otherwise referred to as mobilization elements so as to improve their safety profile.
Additionally elements that enabled maintenance were removed.
Upon finding that the synthetic cloning vectors were unstable antibiotic resistance genes were inserted and used in combination with antibiotics for the selection and maintenance of the plasmids.
Bacteria that lose the plasmid during cell division are killed by the antibiotic whilst those that retain the plasmid express proteins capable of negating the lethal effects of the antibiotic.
The success of this strategy now means that practically all synthetic plasmids in use today contain antibiotic resistance genes.
Recent attempts to increase the biosafety profile of plasmid based therapies have included genetically attenuating vectors so that they have a reduced ability to persist in the host.
This reduction in persistence results in an inability to transfer genetic information.
Earlier studies indicated that synthetic plasmids were not liable to transfer to the natural bacterial population.
However, more recent work has demonstrated that transmission may be possible in the environment of the intestinal tract.
The spread of antibiotic resistance in gram negative bacteria has also been acknowledged to be mostly due to the transfer of plasmids that contain antibiotic resistance genes.
With sufficient numbers of host and recipient bacteria present in the human intestinal tract transfer of self-transmissible plasmids occurs both with and without selection.
The rate of transformation of plasmids has even been shown to be higher in vivo than that can be achieved in vitro.
Non-mobilizable plasmids can in fact be transferred from one bacterium to another in the presence of another, conjugative, plasmid. This even applies if the conjugative plasmid is present in the recipient bacterium.
Many plasmid selection systems today are based on the use of antibiotics and genes that express proteins capable of negating the lethal effects of the antibiotic.
It may be advantageous for example to not to have to use an antibiotic resistance gene in a plasmid due to its inclusion in the plasmid, which may be used in antibiotic treatment or vaccine production.
The use of plasmids in transgenic crops where the antibiotic resistance genes may survive into the intestinal systems of livestock has been brought into question.
In addition the FDA actively discourages the use of antibiotic resistance genes in recombinant plasmid based therapies in order to avoid the accidental release of these genes into the environmental gene pool.
Recombinant plasmid based therapies include but are not limited to gene therapy and recombinant bacteriophage therapy.
In addition the emergence of antibiotic resistant bacteria poses a serious threat. Toxin-antitoxin (TA) systems otherwise known as toxin-antidote (TA) or post-segregational killing (PSK) systems can be found either encoded on plasmids or chromosomally.
They are divided into two broadly distinguishable classes, type I and type II.
Type I encode a small hydrophobic toxic peptide that acts by disrupting membrane function and normally a single antisense sRNA antitoxin. An example of this is the chromosomally encoded dinQ-agrB system. Some type I systems such as the plasmid encoded hok-sok system also contain a second regulatory sRNA.
Type II systems are those in which both the toxin and antitoxin are proteins and the toxin often acts through affecting intracellular activity.
Recently, a third type of TA loci was identified. In this case, the antitoxin is a small cis-encoded RNA that inhibits toxin activity by direct molecular interaction.
The functions of chromosomally encoded TA systems are likely to be quite diverse, depending on the type of TA system, their genomic location and their host species. Plasmid encoded TA systems are required for plasmid replication and maintenance.